There are two distinct regions, the granitic islands, the world's only oceanic islands of granitic rock and the coralline outer islands. The granite islands are the world’s oldest ocean islands, while the outer islands are mainly very young, though the Aldabra group and St Pierre (Farquhar Group) are unusual, raised coral islands that have emerged and submerged several times during their long history, the most recent submergence dating from about 125,000 years ago

The Inner Islands is the collective term for 45 islands with a total area of 247.2 km2, 54% of the Seychelles area but with more than 99% of the population.

The Granitic Group consists of 45 granite islands, all within a 56 km (35 mi) radius of the main island of Mahé. These islands are rocky, and most have a narrow coastal strip and a central range of hills rising as high as 914 metres (2,999 ft). The most important islands of this group are:

Mahé is the largest island, with a size of 156.7 km2 (61 sq mi). Victoria, the capital, is on Mahé.

Millions of years ago, the archipelago was created by a combination of the separation of India from Africa as well as undersea volcanoes similar to those from which Mauritius and Réunion were created. Subsequently the vast majority of this huge land area became submerged over time. Seychelles straddles the eastern portion of the Somali plate.

The climate is equable and healthy, although quite humid, as the islands are small and subject to marine influences. The temperature varies little throughout the year. Temperatures on Mahé vary from 24 to 30 °C (75.2 to 86.0 °F), and rainfall ranges from 2,900 mm (114.2 in) annually at Victoria to 3,600 mm (141.7 in) on the mountain slopes. Precipitation is somewhat less on the other islands. During the coolest months, July and August, it drops to as low as 24 °C (75.2 °F). The southeast trade winds blow regularly from May to November, and this is the most pleasant time of the year. The hot months are from December to April, with higher humidity (80%). March and April are the hottest months, but the temperature seldom exceeds 31 °C (87.8 °F). Most of the islands lie outside the cyclone belt, so high winds are rare.

The uniqueness of the Seychelles' ecology is reflected in the US$1.8 million project of the Global Environment Trust Fund of the World Bank (see Glossary) entitled Biodiversity Conservation and Marine Pollution Abatement, that began in 1993. The World Bank study for this project states that the islands contain, out of a total of 1,170 flowering plants, "at least 75 species of flowering plants, 15 of birds, 3 of mammals, 30 of reptiles and amphibians, and several hundred species of snails, insects, spiders and other invertebrates" found nowhere else. The diversity of species in the islands is being assessed by the Nature Protection Trust of Seychelles. In addition, the waters contain more than 1000 kinds of fish, of which more than one-third are associated with coral reefs. Specific examples of unique birds are the black paradise flycatcher, the black parrot, the brush warbler, and a flightless rail. Most famous of all the Seychelles animals are the giant tortoises of the genus Aldabrachelys.

As a result of extensive shipping to Seychelles that brings needed imports and the discharge of commercial tuna fishing, the waters suffer some pollution. Furthermore, goats brought to Aldabra Islands are destroying much of the vegetation on which giant tortoises feed or seek shade. Rats have reduced biodiversity on many islands. Climate change is also a significant issue; it was recently realised that this has caused the extinction of the endemic snail Rhachistia aldabrae.

Seychelles began addressing the conservation problem in the late 1960s by creating the Nature Conservancy Commission, later renamed the Seychelles National Environment Commission. A system of national parks and animal preserves covering 42% of the land area and about 260 km2 of the surrounding water areas has been set aside. Legislation protects wildlife and bans various destructive practices. In Seychelles' 1990 to 1994 National Development Plan, an effort was made to include in the appropriate economic sectors of the development plan environment and natural resources management aspects.

Also connected with ecology is a World Bank project dealing with the environment and transportation. Launched in 1993 with a loan of US$4.5 million, it is designed to improve the infrastructure of Seychelles with regard to roads and airports or airstrips so as to encourage tourism as a source of income, while simultaneously supporting environmental programs in resource management, conservation, and the elimination of pollution.

Another major project has been funded by Fonds Francais pour l'environnement Mondiale (FFEM) and implemented by Island Conservation Society. This aims to rehabilitate and enhance islands for the maintenance of native biodiversity in Seychelles through eradication of introduced predator species, rehabilitation of habitats and reintroduction of rare or threatened species. Rats have been eliminated from North Island under this project and more schemes are planned, including at Cosmoledo Atoll and on Conception Island.